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Use write_table_points instead of regions #3

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Merged
kkyoda merged 1 commit into from
Mar 21, 2023
Merged

Use write_table_points instead of regions #3

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11 changes: 3 additions & 8 deletions write_kyoda_wormdata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
import numpy as np
from ome_zarr.io import parse_url
import zarr
from ngff_tables_prototype.writer import write_table_regions
from ngff_tables_prototype.writer import write_table_points


df = pd.read_csv('wt-N2-081015-01.csv', names=('t', 'pid', 'cid', 'x', 'y', 'z', 'name', 'sphericity', 'volume', 'phase'))
Expand Down Expand Up @@ -55,8 +55,6 @@


adata = ad.AnnData(X = dfa, obs = obs_meta)
# simple 2D table is suitable for obsm data
adata.obsm["tracking"] = obsp_raw

# write as sparse data to obsp
adata.obsp["tracking"] = csr_matrix(obsp_raw)
Expand All @@ -65,10 +63,7 @@
root = zarr.group(store=store)

tables_group = root.create_group(name="tables")
write_table_regions(
write_table_points(
group=tables_group,
adata=adata,
region="labels/label_image",
region_key=None,
instance_key="cell_id"
adata=adata
)